Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

Article

Penton, C. Ryan, Gupta, V. V. S. R., Tiedje, James M., Neate, Stephen M., Ophel-Keller, Kathy, Gillings, Michael, Harvey, Paul, Pham, Amanda and Roget, David K.. 2014. "Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing." PLoS One. 9 (4), pp. 1-12. https://doi.org/10.1371/journal.pone.0093893
Article Title

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

ERA Journal ID39745
Article CategoryArticle
AuthorsPenton, C. Ryan (Author), Gupta, V. V. S. R. (Author), Tiedje, James M. (Author), Neate, Stephen M. (Author), Ophel-Keller, Kathy (Author), Gillings, Michael (Author), Harvey, Paul (Author), Pham, Amanda (Author) and Roget, David K. (Author)
Journal TitlePLoS One
Journal Citation9 (4), pp. 1-12
Number of Pages12
Year2014
PublisherPublic Library of Science (PLoS)
Place of PublicationSan Francisco, CA. United States
ISSN1932-6203
Digital Object Identifier (DOI)https://doi.org/10.1371/journal.pone.0093893
Abstract

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial
communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere,
subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and
community ordinations revealed significant differences in fungal community composition between suppressive and nonsuppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

KeywordsDNA extraction; endophyte; fungal community; fungal plant disease; fungus identification; Fusarium; gene sequence; geographic distribution; LSU gene; microbial diversity; mycoparasite; Penicillium; plant fungus interaction; pyrosequencing; Rhizoctonia solani; rhizosphere fungus; RNA gene; soil analysis; Xylariales
ANZSRC Field of Research 2020310805. Plant pathology
410603. Soil biology
310703. Microbial ecology
Public Notes

Copyright: 2014 Penton et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Byline AffiliationsMichigan State University, United States
Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
Department of Agriculture, Fisheries and Forestry, Queensland
Department of Primary Industries and Regions, South Australia
Macquarie University
Institution of OriginUniversity of Southern Queensland
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